An Interview with Amy Charkowski

Jan 31, 2014

Professor Amy Charkowski

How did you get involved with potato research?

I had an exceptional high school science teacher, Marilyn Hansen, who helped high school students find volunteer spots in laboratories at the University of Wisconsin-Madison. She connected me with Dr. Steve Slack, who used to work on potatoes at UW-Madison, and I volunteered in his lab for about a year. Mostly, I cut strips of parafilm to wrap around test tubes and other simple tasks, but it gave me the chance to ask lots of questions of the very tolerant people in the Slack lab and to learn what a career in plant sciences might be like.

I later worked with viral and bacterial pathogens that infect beans, tomatoes, and peppers as an undergraduate and graduate student. After graduate school, I started working for USDA in food safety research. I quickly realized that I missed working with plant diseases, so I started looking for a different job. Amazingly, Dr. Slack’s job was open at that time, and I ended up back with potatoes and leading the same program where I had my first job in science.

What does your research in potatoes focus on?

Initially, we focused on how bacteria cause disease in potato, specifically, how Pectobacterium causes potatoes to wilt and rot. As I learned more about potatoes and potato farming, it became clear that there was a need to learn more about how to grow potatoes on small organic farms, and how potatoes resist disease. My lab’s focus has shifted more toward trying to find environmentally friendly ways to control common potato diseases. The best way for farmers to control disease is to use resistant varieties. However, there is very little information available on which pests and diseases are most important for organic farmers in the Midwest and which varieties do the best on organic farms, so we decided to address parts of these questions. We still have a strong interest in Pectobacterium and bacterial soft rot, however, and are trying to map potato genes that provide resistance to this disease.

What is most challenging about breeding potatoes?

There are many challenges! Potato genetics are complicated, and there have been relatively little investment and progress into understanding how different potato genes contribute to important characteristics compared to other major crops. Potatoes are also very sensitive to the environment that they are grown in, so yield and quality can vary tremendously from year to year and from location to location, particularly on organic farms.

The methods that potato breeders use have changed little in the past century. When you do things the same way for a long time, you get essentially the same results. Potato quality has improved, but there have been no significant changes in pest and disease resistance or yield when new and heirloom varieties are compared. For example, Russet Burbank is still one of the most popular varieties grown today, and it originated in the late 1800s.

One of the challenges in potato breeding is that potatoes are vegetatively propagated, and they are susceptible to many diseases spread by potato tubers. Once a parent plant becomes infected, all of the progeny from that plant are also infected. Therefore, to get a good assessment of their varieties, potato breeders need to keep their plants disease free, which is very difficult. Therefore, potato breeders often have to try to assess potato varieties that are infected with viruses, which is also a difficult task.

Potato plants in flower

We were initially interested in trialing heirloom varieties rather than potato breeding. Bacterial and viral diseases were also a problem with heirloom varieties since there were no disease-free plants available for many interesting heirloom potato lines. We received a USDA-OREI grant to cure 100 heirloom lines and to trial these lines on organic farms. Over the past few years, we have built a network of nearly 30 farmer partners, from Ohio to North Dakota, and these farmers have helped us trial both heirloom and new lines on their farms. We will be working with this group again in 2014, and are always interested in adding new farmers to this group.

These variety trials have helped us identify varieties that have characteristics useful on organic farms, such as leafhopper resistance or virus resistance. Building the farmer network has helped us trial lines under many environmental conditions to identify lines that are robust in many environments.

Why do we need potato varieties that are specifically bred for organic cultivation? What are the specific challenges in potato farming that organic farmers face?

On organic farms, it is more important to have potato varieties that have good pest and disease resistance and that efficiently use nutrients from soil organic matter. Some farmers also prefer potatoes with unique shapes, colors, or flavors.

Some of the pest and disease challenges that organic potato farmers face are the same as conventional farmers. For example, the disease late blight, early blight, and Verticillium wilt are problems on any type of potato farm. However, organic farmers must use different methods to reduce losses from these diseases, so they tend to be more interested in disease resistance for these common diseases than conventional farmers.

Some pest and disease challenges appear to be more significant on organic farms. For example, potato leafhoppers can cause large yield losses when they feed on potatoes. Synthetic systemic insecticides control leafhoppers on conventional farms, but insecticides approved for use on certified organic farms are less effective. As a result, we see that potato varieties with leafhopper resistance perform much better on organic farms than potatoes that lack resistance. Unfortunately, because leafhoppers are not a problem for conventional farmers, very little effort has gone into breeding for resistance or understanding how some varieties resist this pest insect.

Professor Charkowski checks to see how her potatoes are growing

What would be the biggest success for organic potato breeding?

Plant breeders are never finished with their job. Consumer preferences, the environment, and pests and pathogens are constantly changing. For these reasons, plant breeders are constantly working to develop improved varieties.

For me, the biggest long-term success for organic potato breeding would not be a particular variety or the discovery of a set of potato genes with a useful function. Rather, it would be for the organic vegetable farm community to work together with students and scientists to reach two goals. One goal would be for organic farmers to breed their own potato varieties. Universities and other organizations could support this work by providing training, useful parent potato lines, and access to new information about potatoes. In turn, the farmers could help students learn about plant sciences, and help scientists identify new challenges in potato farming or interesting new plant phenotypes that might lead to new discoveries in biology.

Some of the varieties of potatoes that Professor Charkowski studies

What does the future hold for organic potato cultivation?

I expect that potato cultivation will continue to be challenging, but I hope that we see an expansion in the number of farmers who grow potato and the number of varieties that we see in stores, at farmers’ markets, and in CSA boxes.

Are there any other areas in the organic field that you’re excited about lately?

There are so many interesting questions related to organic farming that it can be difficult to focus on just a few of them. I have worked for most of my career with plant pathogenic microbes, and I enjoy learning about how bacteria interact with plants. Over the past 20 years, there have been many important discoveries in how plant pathogens manipulate plant cells and cause disease. However, we still have a tremendous amount to learn about how beneficial soil and leaf-dwelling microbes affect plant health. I think that, over the next few decades, there will be a shift in scientific effort toward understanding how microbes do things like protect plants from disease and abiotic stresses, such as drought. Like variety trialing and plant breeding, I think that this is another area where organic farmers will be able to partner with researchers to help guide this work.